AW: Re: Re: Re: NAMD 2.11b1 released

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Nov 27 2015 - 01:22:44 CST

This indicates, that you set the parameter after a „run“ or „minimize“ command, just set it before in your script.

 

 

Norman Geist

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von sunyeping
Gesendet: Freitag, 27. November 2015 06:27
An: namd-l <namd-l_at_ks.uiuc.edu>; Jim Phillips <jim_at_ks.uiuc.edu>
Betreff: namd-l: Re: namd-l: Re: namd-l: Re: namd-l: NAMD 2.11b1 released

 

When include "twoAwayX yes" in the conf file, I get the error:

 

Reason: FATAL ERROR: Setting parameter twoAwayX from script failed!

 

Actually it is not just for 2.11b1. Early version is the same. What's wrong?

 

Yeping

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From:Jim Phillips < <mailto:jim_at_ks.uiuc.edu> jim_at_ks.uiuc.edu>

Time:2015 Nov 13 (Fri) 12:47

To:namd-l < <mailto:namd-l_at_ks.uiuc.edu> namd-l_at_ks.uiuc.edu>, 孙业平 < <mailto:sunyeping_at_aliyun.com> sunyeping_at_aliyun.com>

Subject:Re: namd-l: Re: namd-l: Re: namd-l: NAMD 2.11b1 released

 

2.11 does support twoAwayX/Y/Z. What are you seeing that suggests not?

Jim

On Fri, 13 Nov 2015, sunyeping wrote:

> And 2.11 version does not seem to support "twoawayx/y/z" option.
Yeping ------------------------------------------------------------------From:Jim Phillips <jim_at_ks.uiuc.edu <mailto:jim_at_ks.uiuc.edu> >Time:2015 Nov 12 (Thu) 20:55To:namd-l <namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu> >, 孙业平 <sunyeping_at_aliyun.com <mailto:sunyeping_at_aliyun.com> >Subject:Re: namd-l: Re: namd-l: NAMD 2.11b1 released

If you were limited by the CPU in 2.10 you're probably still limited by
the CPU in 2.11. The largest increases are for energy evaluation and
implicit solvent. Explicit solvent force evaluation is closer to 30%.
We'll be working to reduce CPU dependence for 2.12.

Jim

On Thu, 12 Nov 2015, sunyeping wrote:

> I have tried this new release of NAMD on my system which has two C2050 GPU. The simulation system contains more than 40,000 atoms but I don't see obvious speedup of the 2.11b1 compared to the CVS-2015-09-29 version. The speed are both around 0.11day/ns. So in what circumstance would the new version increase GPU performance?
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
------------------------------------------------------------------From:Tristan Croll <tristan.croll_at_qut.edu.au <mailto:tristan.croll_at_qut.edu.au> >Time:2015 Nov 12 (Thu) 10:12To:namd-l <namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu> >, Jim Phillips <jim_at_ks.uiuc.edu <mailto:jim_at_ks.uiuc.edu> >Subject:Re: namd-l: NAMD 2.11b1 released
Hi Jim,

A doubling of CUDA performance is very exciting! Are the best speed-ups seen in smaller or larger systems?

Thanks,

Tristan

________________________________________
From: owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu> <owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu> > on behalf of Jim Phillips <jim_at_ks.uiuc.edu <mailto:jim_at_ks.uiuc.edu> >
Sent: Wednesday, 11 November 2015 1:39 AM
To: namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>
Subject: namd-l: NAMD 2.11b1 released

Dear NAMD users,

NAMD 2.11b1 is available for download (since last night), with many new
features noted below. This is a beta release, so please test your
simulations over the next few weeks and let us know of any issues. I am
hoping for a short beta cycle with limited new code (and some new
documentation) added before the final 2.11 release.

Thank you all for your efforts and support.

Jim

+--------------------------------------------------------------------+
| |
| NAMD 2.11b1 Release Announcement |
| |
+--------------------------------------------------------------------+

                                                     November 10, 2015

The Theoretical and Computational Biophysics Group at the University of
Illinois is proud to announce the public release of a new version of
NAMD, a parallel, object-oriented molecular dynamics code designed for
high-performance simulation of large biomolecular systems. NAMD is
distributed free of charge and includes source code. NAMD development
is supported by the NIH National Institute of General Medical Sciences.

NAMD 2.11 has many advantages over NAMD 2.10, among these are:

- GPU-accelerated simulations up to twice as fast as NAMD 2.10

- Enhanced Tcl scripting of collective variables and "cv" command

- Collective variables module improvements including to histogram bias

- TclForces query total net forces for atom groups

- Replica-exchange multiplexing (fewer partitions than replicas)

- Tcl scripting multiple in-memory checkpoints

- Improved Tcl scripting multi-copy interface documentation

- Tcl scripting asynchronous multi-copy remote in-memory checkpoints

- Tcl scripting asynchronous multi-copy remote trajectory output

- Tcl scripting asynchronous multi-copy remote script evaluation

- Tcl scripting asynchronous multi-copy central work queue support

- Tcl scripting asynchronous multi-copy workflow-style programming

- Improved minimization for Drude force field and rigid bonds

- Improved long-range LJ correction with VDW force switching

- Improved alchemical calculations with VDW force switching

- Pressure calculation with fixed atoms on GPU works as on CPU

- Improved scaling for GPU-accelerated particle-mesh Ewald calculation

- Improved scaling for GPU-accelerated simulations

- Improved scaling for multi-threaded "smp" builds

- Prevent running smp builds with one thread per process

- Support trajectory files larger than 2GB on Windows

- Improved Intel Xeon Phi coprocessor support

- Update to Charm++ 6.7.0 with improved multi-copy support

- Ignore ioformat statement in CHARMM topology and parameter files

- Psfgen improvements including long resids and insertion codes

- Psfgen package available in NAMD Tcl interpreter

Details at http://www.ks.uiuc.edu/Research/namd/2.11/features.html

NAMD is available from http://www.ks.uiuc.edu/Research/namd/

For your convenience, NAMD has been ported to and will be installed
on the machines at the NSF-sponsored national supercomputing centers.
If you are planning substantial simulation work of an academic nature
you should apply for these resources. Benchmarks for your proposal
are available at http://www.ks.uiuc.edu/Research/namd/performance.html

The Theoretical and Computational Biophysics Group encourages NAMD users
to be closely involved in the development process through reporting
bugs, contributing fixes, periodical surveys and via other means.
Questions or comments may be directed to namd_at_ks.uiuc.edu <mailto:namd_at_ks.uiuc.edu> .

We are eager to hear from you, and thank you for using our software!

 

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